Lake Winnebago is located at 38°49'45" North, 94°22'1" West (38.829238, -94.366989).

According to the United States Census Bureau, the city has a total area of 2.30 mi2 (5.96 km2). 1.88 mi2 (4.88 km2) of it is land and 0.42 mi2 (1.08 km2) of it is covered by water. The total area is 18.06% water.

Lake Winnebago is located in the Central Standard Time (CST) timezone, GMT-06:00. It observes Daylight Saving Time (DST).